Focusing on Polish and European population genetics and modern physical anthropology.

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Monday, December 21, 2015

Bronze Age steppe warrior affinity test

Reich Lab et al. are now targeting more than 1.2 million sites in the ancient samples that they genotype, including over one million from the Illumina genotype array. This is great because it means that I can now run analyses with these ancients on the present-day populations in my Illumina array-based dataset using as many as 500K SNPs, which makes things more accurate and interesting.
Below are a few sets of D-statistics of the form D(Outgroup,X)(Population1,Population2), featuring several ancient populations from the recent Allentoft et al., Haak et al. and Mathieson et al. papers. I'm basically testing how much closer X is to either Population1 or Population2.
The results look very solid considering the spatio-temporal and archaeological origins of the samples. However, the outcomes for the smaller Northern European nations perhaps look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem.

15 comments:

"At the same time, however, the outcomes for the smaller Northern European nations look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem."

The inflation of Kalash D-stats towards Brahui in a similar test was detectable by comparing their IBS sharing with Brahui (not elevated) to their D-stat result, you might want to try testing IBS sharing with ancients using these same SNP's.

Regarding the effect of homogenousness in particular, I guess the way to test that would be to check the internal IBS-sharing of every modern sample, or maybe just modern North, East and Central European sample in this case. Then check the sample's two individuals with highest and lowest IBS sharing with ancients, heterogenous populations should show a wider gap between these two but the "highest" sharer might be above those in homozygous pops.

Do all LNBA North Europeans, including Nordic LNBA and the Urnfield guy, have more Steppe than modern North Europeans? Are most Bell beaker more Steppe than Unetice? Is Unetice more Steppe than Nordic LNBA? Is Nordic LN more Steppe than Nordic BA and IA? Are the Bell Beaker the least homogeneous LNBA European group?

The Nordic LNBA samples aren't very homogeneous. Some show a lot more steppe ancestry than modern Scandinavians, and others much less. But overall, Nordic LNBA shows a little more steppe ancestry than modern Scandinavians. You can see that here, because it's a little higher than Norwegians and Swedes.

It's surprising 1800 years after arrival some were still overwhelmingly Steppe. Do you think it is only WHG and EEf which is pulling modern Northern Europeans further away from the Steppe, or also excess CHG? Does 50-70% replacement levels in Scandinavia and British Isles by Eastern/Steppe(admixed with MN) populations sound realistic?

Something is very odd here. How have some Ukrainians, Kargopol Russians and Erzya less affinity to Sintashta than French Basques? Many results for East Europeans look very odd.Homogeneity of some West Europeans and non homogeneity of many East Europeans makes this lists inaccurate.

Ok that makes sense for siberian-admixed people but why are Ukrainians also so low in this list. Lower than Slovakians, all West Europeans and even Slovenians? Russians and Belarusians are also lower in the list than I would except.

Yes that is obvious from admixture and the more southern location of Ukraine. I was not questioning that but rather how Poltava Ukrainians have less or the same Sintashta affinity like French Basques. Here Ukrainians look often more southern than Slovakians and even Slovenians what is rather surprising for me. Ukrainians should have similar amounts of Steppe admixture like Irish, Scots and some Norwegians and Belarusians and Russians should have a bit more steppe admixture than Norwegians based on their higher EHG.

It is strange that Scythian affinity is according to this not peaking in the Volga region today, where scythian Z2123 is still found unlike in the rest of Europe and where Scythians had a very very long presence. I still have my doubts about Scythian affinty being higher in NW Europe than in the Volga region. Scythians left hardly any descendants in Europe outside of the Volga region and were very Siberian admixed compared to most modern Europeans. So their admixture proportions should be similar to Erzya/Moksha/Kargopol Russians .

CHG is higher in The Balkan, Ukraine and not low in The Volga Region. Actually admixture (CHG K8 on anthrogenica) showed that it is not higher in NW Europe and quite high among Volga people. The ratio of EEF/CHG is much higher in West Europe than in East Europe. Tatars with confirmed direct scythian ancestry (They carry R1a-Z2123 like Scythians and absent in the rest of Europe) have lower or the same affinity to Volga Scythians than Albanian and Spaniards here. That is really against any common sense especially because these Scythians had a lot Siberian admixture absent among almost all other Europeans . Admixture clearly showed that these Scythians were basically like modern Tatars but with a higher CHG and EHG affinity and that makes quite much sense.

Anyways thanks very much for your analysis. It is a mystery and something almost in all of Far East Europe is dampening the affinity. Volga Finns who should have similar admixture proportions,who lack significant altaic admixture and who have a lot of EHG for modern european standards, are also much lower in the list than i expected. So either something is inaccurate or something which effected all of East Europe lowered the affinity but i dont think it were Altaics because Volga Finns dont seem to have that much altaic admixture like Russians who also basically lack it. Admixture, which is probably not always reliable, rather showed that the closest population to modern Scythians were Volga Finns, Tatars and Far East Europeans (lithuanian-like with siberian admixture) but yes you are right without more genomes we can not solve this mystery.